Surface transient electromagnetic (TEM) data with large transmitter loops for deep mineral exploration are often complicated by the non-trivial coupling between extended sources and arbitrarily oriented geological targets. This case study reports a TEM field data set acquired across terranes with strong lateral inhomogeneity, which is responsible for the high inconsistency in TEM data patterns along the survey line, as well as for the negative TEM transients (sign reversal) at some near-central loop stations. 3D forward modeling and inversion, as maturing tools in recent years, offer unique opportunities to extract as much geological information from such data as possible. 3D forward simulations of representative synthetic models found that the phenomenon of sign reversal at some TEM stations is associated with compact conductors enclosed by the transmitter loop and receivers that are in the loop, but off the conductor–a situation that is common in large-loop TEM and can only be explained by 3D models. However, 3D inversion of the field data with a uniform subspace as the initial and reference model fails to converge, another point of evidence that 3D inversions of large-loop TEM data are more likely to be subject to stability issues. Our solution is to warm-start the inversion with the representative model in the forward simulation experiments as the initial model, so the ill-posed 3D inversion can escape from local minima. Finally, the vertical contact structure in our 3D-inversion model is verified by a resistivity cross section of the CSAMT method. Our case study demonstrates the demand and capability of 3D electromagnetic modeling and inversion for high-resolution deep mineral exploration. It also provides an easy-to-follow template for carrying out 3D interpretation for complex geology in practice.